Prosecutors in Minnesota filed criminal charges on Friday against the Roman Catholic Archdiocese of St. Paul and Minneapolis, accusing church leaders of mishandling repeated complaints of sexual misconduct against a priest and failing to follow through on pledges to protect children and root out pedophile clergymen.

The charges and accompanying civil petition, announced by the Ramsey County prosecutor, John J. Choi, stem from accusations by three male victims who say that from 2008 to 2010, when they were under age, a local priest, Curtis Wehmeyer, gave them alcohol and drugs before sexually assaulting them.

The criminal case amounts to a sweeping condemnation of the archdiocese and how its leaders have handled the abuse allegations — even after reforms were put in place by church leaders to increase accountability — and the charges are among the most severe actions taken by American authorities against a Catholic diocese.

“Today, we are alleging a disturbing institutional and systemic pattern of behavior committed by the highest levels of leadership of the Archdiocese of St. Paul and Minneapolis over the course of decades,” Mr. Choi said in a statement.

Curtis Wehmeyer, a former priest in Minnesota, was sentenced in 2013 for criminal sexual conduct and possession of child pornography.

Mr. Wehmeyer, 50, who was dismissed as a priest in March, was sentenced to five years in a Minnesota prison in 2013 for criminal sexual conduct and possession of child pornography. He also has been charged with sex crimes in Wisconsin.

The six criminal charges filed Friday, misdemeanors with a maximum fine of $3,000 each, accused the archdiocese of failing to protect children. Mr. Choi also filed a civil petition against the archdiocese that he said was intended to provide legal remedies to prevent similar inaction from happening again.

The 44-page criminal complaint states that concerns about Mr. Wehmeyer date to the 1990s, when he was in seminary and supervisors suggested that his past sexual promiscuity and alcohol abuse made him a poor candidate for the priesthood.

Fellow clergy members and parishioners voiced repeated concerns about Mr. Wehmeyer after his ordination in 2001, prosecutors said. The archdiocese allowed Mr. Wehmeyer to continue as a priest, and even placed him in charge of his own parish, despite learning about his attempts to pick up young men at bookstores and his encounters with law enforcement at known “cruising” spots where men were known to meet other men for anonymous sexual encounters.

The charging documents also say that archdiocese officials knew that Mr. Wehmeyer used a boys’ bathroom at a parish elementary school instead of the staff restroom; tried to give an elementary-age boy a tour of the rectory in violation of policy; and took camping trips with boys where some of the sexual abuse was said to have occurred.

The archdiocese placed Mr. Wehmeyer in a monitoring program for priests facing complaints of abuse or other problems, but prosecutors said in court documents that the supervision and follow-through was “lax or nonexistent.”

“The archdiocese’s failures have caused great suffering by the victims and their family and betrayed our entire community,” Mr. Choi said in his statement.

Civil cases against the archdiocese and priests have poured in since 2013, when the Minnesota State Legislature passed the Child Victims Act, which opened a three-year window for filing lawsuits involving claims of sexual abuse that were beyond the criminal statute of limitations.

Many people have made such claims since that law’s passage, bringing new attention to decades-old cases, and creating public records of accusations against some priests.

David Clohessy, director of the Survivors Network of Those Abused by Priests, said he was pleased by the indictment, “but the credit goes to Minnesota lawmakers, not this prosecutor.”

An auxiliary bishop for the diocese, Andrew Cozzens, said in a statement Friday, “We deeply regret the abuse that was suffered by the victims of Curtis Wehmeyer and are grieved for all victims of sexual abuse.”

He added that the archdiocese would continue to cooperate with prosecutors. “We all share the same goal: to provide safe environments for all children in our churches and in our communities,” Bishop Cozzens said.

Criminal prosecution of an entire Catholic archdiocese is rare, but not entirely unprecedented, in American courts.

An Ohio judge in 2003 convicted the Archdiocese of Cincinnati of failing to report sexually abusive priests in the 1970s and ’80s. The judge fined the archdiocese $10,000, the maximum allowed, after the archbishop entered a no-contest plea.

But the Minnesota allegations are especially stark because the sexual abuse is said to have occurred relatively recently, long after sexual misconduct by priests had been widely reported and after Catholic institutions implemented programs aimed at preventing further abuse.

“Naming the archdiocese as a corporation implicates the wrongdoing and the failure to protect children by all of the top officials, past and present,” Jeff Anderson, a lawyer in Minnesota who has represented clergy sex-abuse victims, said in a statement.